Dear Dr. Fred,

Thank you for your choice to try motifStack. When you using MacBook, just try motifStack without setting R_GSCMD.

For linux system or mac,  a GhostScript executable will be searched by name on your path when R_GSCMD is unset. You can also try to use command:
which gs
in you terminal.

In my case, my GhostScript is installed at "/usr/local/bin/gs"
And you can try Sys.setenv(R_GSCMD="/usr/local/bin/gs") before draw motifs or just do not set this for a mac.

For window 7, I will copy my code to you later.

Good luck.

Yours sincerely,

Jianhong Ou

LRB 670A
Program in Gene Function and Expression
364 Plantation Street Worcester,
MA 01605

From: <Mills>, Frederick <Frederick.Mills@fda.hhs.gov<mailto:Frederick.Mills@fda.hhs.gov>>
Date: Friday, December 13, 2013 2:51 PM
To: Jianhong Ou <jianhong.ou@umassmed.edu<mailto:jianhong.ou@umassmed.edu>>
Subject: MotifStack not plotting?

Dear Dr. Ou,

Not sure if I should address this to you or bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>.  I having an issue on one Ubuntu/R-Bioconductor installation with motitStack.
 I installed Biolinux on a partition on my iMac, giving me Ubuntu 12.04.  Upgraded to R 3.01, Bioconductor Workflow install, BiocLite, and installed the following
source("http://bioconductor.org/biocLite.R"<http://bioconductor.org/biocLite.R%22>) biocLite(c("MotifDb", "GenomicFeatures", "TxDb.Scerevisiae.UCSC.sacCer3.sgdGene","org.Sc.sgd.db", "BSgenome.Scerevisiae.UCSC.sacCer3", "motifStack", "seqLogo")-as per the Bioconductor examples for TF binding sites.  Also grImport and MotIV.   I set the R working directory as setwd( /usr/local/lib/R/site-library and the Ghostscript executable is at /usr/bin/ghostscript. motifStack works fine with this installation.

However, I have  a MacBook Pro at home on which I've installed Ubuntu 13.10, and then installed R 3.01, and then the same packages as above. I also set the R working directory as above and Ghostacript is at the same location.  Everything works except motifStack, which opens a blank plot window and gives the following errors.


Error in grImport::PostScriptTrace(paste(psfilename, ".ps", sep = ""),  : status 1 in running command '/usr/bin/ghostscript -q -dBATCH -dNOPAUSE -sDEVICE=pswrite -sOutputFile=/dev/null -sstdout=/tmp/Rtmp8UuHLT/filea5a4df42eac.xml capturefilea5a4df42eac.ps

If I run the above command in terminal, still no luck.  I've tried setting the environment with Sys.setenv(R_GSCMD="/usr/bin/gs")-same result. Running Ghostscript from the terminal opens a blank plot window, as does running grid within R.

I've had a very similar experience trying to use motifStack in a Windows 7 environment.

Anyway, not an absolute necessity, but it would be great if I could get this second installation working.

Thanks very much,

Fred Mills, Ph.D. Staff Scientist

FDA, CDER

NIH Campus, Bethesda, MD




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